add "example" python class for database generation

examples/NavierStokesDB.py

+#######################################################################
+#                                                                     #
+#  Copyright 2015 Max Planck Institute                                #
+#                 for Dynamics and Self-Organization                  #
+#                                                                     #
+#  This file is part of bfps.                                         #
+#                                                                     #
+#  bfps is free software: you can redistribute it and/or modify       #
+#  it under the terms of the GNU General Public License as published  #
+#  by the Free Software Foundation, either version 3 of the License,  #
+#  or (at your option) any later version.                             #
+#                                                                     #
+#  bfps is distributed in the hope that it will be useful,            #
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of     #
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the      #
+#  GNU General Public License for more details.                       #
+#                                                                     #
+#  You should have received a copy of the GNU General Public License  #
+#  along with bfps.  If not, see <http://www.gnu.org/licenses/>       #
+#                                                                     #
+# Contact: Cristian.Lalescu@ds.mpg.de                                 #
+#                                                                     #
+#######################################################################
+
+
+
+import os
+import h5py
+import bfps
+
+class NavierStokesDB(bfps.NavierStokes):
+    """
+        Example of how bfps is envisioned to be used.
+        Standard NavierStokes class is inherited, and then new functionality
+        added on top.
+        In particular, this class will generate an HDF5 file containing a 5D
+        array representing the time history of the velocity field.
+        Snapshots are saved every "niter_stat" iterations.
+
+        No effort was spent on optimizing the HDF5 file access, since the code
+        was only used for a teeny DNS of 72^3 so far.
+    """
+    standard_names = ['NSDB',
+                      'NSDB-single',
+                      'NSDB-double']
+    def __init__(
+            self,
+            name = 'NavierStokesDataBase-v' + bfps.__version__,
+            **kwargs):
+        bfps.NavierStokes.__init__(
+                self,
+                name = name,
+                **kwargs)
+        self.file_datasets_grow += """
+                {
+                    if (myrank == 0)
+                    {
+                        hid_t database_file;
+                        char dbfname[256];
+                        sprintf(dbfname, "%s_field_database.h5", simname);
+                        database_file = H5Fopen(dbfname, H5F_ACC_RDWR, H5P_DEFAULT);
+                        hsize_t dset = H5Dopen(database_file, "rvelocity", H5P_DEFAULT);
+                        grow_single_dataset(dset, niter_todo/niter_stat);
+                        H5Dclose(dset);
+                        H5Fclose(database_file);
+                    }
+                }
+                """
+        self.stat_src += """
+                {
+                    fs->compute_velocity(fs->cvorticity);
+                    *tmp_vec_field = fs->cvelocity;
+                    tmp_vec_field->ift();
+                    char dbfname[256];
+                    sprintf(dbfname, "%s_field_database.h5", simname);
+                    tmp_vec_field->io(dbfname, "rvelocity", fs->iteration / niter_stat, false);
+                }
+                """
+        return None
+    def get_database_file_name(self):
+        return os.path.join(self.work_dir, self.simname + '_field_database.h5')
+    def get_database_file(self):
+        return h5py.File(self.get_postprocess_file_name(), 'r')
+    def write_par(
+            self,
+            iter0 = 0,
+            **kwargs):
+        bfps.NavierStokes.write_par(
+                self,
+                iter0 = iter0,
+                **kwargs)
+        with h5py.File(self.get_database_file_name(), 'a') as ofile:
+            ofile.create_dataset(
+                    'rvelocity',
+                    (1,
+                     self.parameters['nz'],
+                     self.parameters['ny'],
+                     self.parameters['nx'],
+                     3),
+                    chunks = (1,
+                              self.parameters['nz'],
+                              self.parameters['ny'],
+                              self.parameters['nx'],
+                              3),
+                    maxshape = (None,
+                                self.parameters['nz'],
+                                self.parameters['ny'],
+                                self.parameters['nx'],
+                                3),
+                    dtype = self.rtype)
+        return None
+